Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A9 F1 I2 R1 760 52.7 2744488 90.2% 2475528 105.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,737,495 G→A *114* (TAG→TAA)  raiA → cold shock protein associated with 30S ribosomal subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,737,4950GA97.9% 144.4 / ‑6.4 47*114* (TAG→TAA) raiAcold shock protein associated with 30S ribosomal subunit
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (18/28);  total (19/28)
Fisher's exact test for biased strand distribution p-value = 4.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATGTACACCGCAATTAACGAATTGATCAACAAGCTGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAGTCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCT  >  NC_000913/2737361‑2737629
                                                                                                                                      |                                                                                                                                      
atGTACACCGCAATTAACGAATTGATCAACAAGCTGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCATCATCGGTGAGAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCt                                                                                                                                    <  1:844143/139‑1 (MQ=255)
        cGCAATTAACGAATTGATCAACAAGCTGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTg                                                                                                                            >  2:86875/1‑139 (MQ=255)
        cGCAATTAACGAATTGATCAACAAGCTGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTg                                                                                                                            <  2:1291398/139‑1 (MQ=255)
          cAATTAACGAATTGATCAACAAGCTGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAg                                                                                                                          >  2:620182/1‑139 (MQ=255)
                                  tGGGACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTGCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGgc                                                                                                  >  1:880529/1‑139 (MQ=255)
                                  tGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCt                                                                                                                                    <  2:643991/105‑1 (MQ=255)
                                  tGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCt                                                                                                                                    >  1:643991/1‑105 (MQ=255)
                                      aCGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGt                                                                                              <  1:513720/139‑1 (MQ=255)
                                      aCGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCACCTTCGGGCGCGt                                                                                              <  1:1030986/139‑1 (MQ=255)
                                          cAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGttttt                                                                                          >  2:398903/1‑139 (MQ=255)
                                                      cTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGt                                                                              <  1:123072/139‑1 (MQ=255)
                                                       tGCATCACAACGACGAAAAACATCGTGCCGCTACAACGGTGAAAGAAGCCAACTTCGTCGAAGAAGATGAAGAAGAGTAGTACTTTATATTGACTGTACCACAAACGCGCCATAGGGGGCGTTATTTGTTGATAGCgga                                                                             >  1:178879/1‑137 (MQ=255)
                                                         cagcaCAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGaa                                                                           <  2:679630/139‑1 (MQ=255)
                                                          agcaCAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGaaa                                                                          >  2:343597/1‑139 (MQ=255)
                                                          agcaCAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGaaa                                                                          >  2:414397/1‑139 (MQ=255)
                                                            cacaAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAAc                                                                        >  1:756229/1‑139 (MQ=255)
                                                                   gCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAAGCCTTTAGATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACgg                                                                 <  1:690884/139‑1 (MQ=255)
                                                                    cGAAGTACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACggg                                                                <  2:641944/139‑1 (MQ=255)
                                                                    cGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACggg                                                                <  2:319272/139‑1 (MQ=255)
                                                                      aaGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTta                                                                                                                                 <  1:939483/72‑1 (MQ=255)
                                                                      aaGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTta                                                                                                                                 >  2:939483/1‑72 (MQ=255)
                                                                      aaGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAg                                                                                                                          >  1:1099236/1‑79 (MQ=255)
                                                                      aaGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAg                                                                                                                          <  2:1099236/79‑1 (MQ=255)
                                                                      aaGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGgta                                                              <  2:756229/139‑1 (MQ=255)
                                                                      aaGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGgta                                                              <  1:86875/139‑1 (MQ=255)
                                                                       aGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGgtac                                                             <  1:620182/139‑1 (MQ=255)
                                                                             tcgtGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCt                                                                                                                                    <  1:308906/62‑1 (MQ=255)
                                                                             tcgtGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCt                                                                                                                                    >  2:308906/1‑62 (MQ=255)
                                                                             tcgtGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAAc                                                                        >  2:377302/1‑122 (MQ=255)
                                                                             tcgtGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAAc                                                                        <  1:377302/122‑1 (MQ=255)
                                                                              cgtGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGACGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTAc                                                                   <  1:877988/126‑1 (MQ=255)
                                                                              cgtGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTCTTGACAGCGTGAAAACAGTAc                                                                   >  2:877988/1‑126 (MQ=255)
                                                                                tGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTaaa                                                    <  1:931289/139‑1 (MQ=255)
                                                                                  ccGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGt                                                  <  1:414397/139‑1 (MQ=255)
                                                                                  ccGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGt                                                  <  1:343597/139‑1 (MQ=255)
                                                                                                aaaGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGaa                                                                           <  2:1295891/100‑1 (MQ=255)
                                                                                                aaaGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGaa                                                                           >  1:1295891/1‑100 (MQ=255)
                                                                                                     cGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACggg                                                                <  2:934995/106‑1 (MQ=255)
                                                                                                     cGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACggg                                                                >  1:934995/1‑106 (MQ=255)
                                                                                                       ccAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGt                                                                                              <  1:439972/74‑1 (MQ=255)
                                                                                                       ccAACTTCGTCGAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGt                                                                                              >  2:439972/1‑74 (MQ=255)
                                                                                                              cgtcgAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGaaaca                                    >  1:758221/1‑125 (MQ=255)
                                                                                                              cgtcgAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGaaaca                                    <  2:758221/125‑1 (MQ=255)
                                                                                                               gtcgAAGAAGTTGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATa                     <  1:398903/139‑1 (MQ=255)
                                                                                                                      aagATGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGtttt              <  2:880529/139‑1 (MQ=255)
                                                                                                                         ttGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTAc                                                                   >  2:1035314/1‑83 (MQ=255)
                                                                                                                         ttGAAGAAGAGTAATCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTAc                                                                   <  1:1035314/83‑1 (MQ=255)
                                                                                                                                  agtaatCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCt  >  2:737905/1‑139 (MQ=255)
                                                                                                                                      |                                                                                                                                      
ATGTACACCGCAATTAACGAATTGATCAACAAGCTGGAACGGCAGCTCAATAAACTGCAGCACAAAGGCGAAGCACGTCGTGCCGCAACATCGGTGAAAGACGCCAACTTCGTCGAAGAAGTTGAAGAAGAGTAGTCCTTTATATTGAGTGTATCGCCAACGCGCCTTCGGGCGCGTTTTTTGTTGACAGCGTGAAAACAGTACGGGTACTGTACTAAAGTCACTTAAGGAAACAAACATGAAACACATACCGTTTTTCTTCGCATTCT  >  NC_000913/2737361‑2737629

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A